These healthy carrot cake muffins have all the flavors of a classic carrot cake, but in muffin size. Made with healthy ingredients, these muffins are a healthy option for a quick snack or breakfast on the go.
We like to keep some homemade muffins for a quick snack. However, not all muffin recipes are created equal, so I developed this healthy carrot cake muffin recipe that’s packed with whole grains, gluten-free, and naturally sweetened with maple syrup.
Even though they are made with healthier ingredients, they still taste delicious. Your whole family is sure to love them!
Muffin recipes like this freeze well, so sometimes I like to make a double batch so I only have to clean the kitchen once – while still stocking up on a healthy snack option.
Make this recipe your own by incorporating other mix-ins like nuts or shredded coconut.
What Makes These Carrot Cake Muffins Healthy?
While everyone has a slightly different definition of what healthy means to them personally, here are some of the reasons we love these healthier carrot cake muffins.
- Swap all-purpose flour for oat flour and almond flour. Oats are a whole grain and are associated with all kinds of health benefits, such as lowering cholesterol. Use certified gluten-free oats (or oat flour) and these muffins will be gluten-free.
- By using almond flour, eggs, and yogurt in these muffins, they have a little more protein than traditional carrot cake muffin recipes.
- Pure maple syrup replaces refined sugar so they’re naturally sweetened.
- These muffins are made with a healthier oil like olive oil or avocado oil that have less saturated fat instead of the butter sometimes used in traditional carrot cake muffin recipes.
Ingredients for healthy carrot cake muffins
All you need are a few basic ingredients to make these healthy carrot cake muffins.
- Oatmeal: Using oat flour instead of all-purpose flour is a great way to incorporate more whole grains into your muffins. If you can’t find oat flour, you can easily make your own. Simply add the oats to a high-powered blender and blend for about 1 minute until a fine flour forms.
- Almond flour: adds protein and healthy fats to these muffins while also making them tender.
- Baking powder & baking soda: it adds enough lift to this muffin recipe so they rise nicely in the oven.
- Spices (ground cinnamon, ginger, nutmeg): a classic combination of spices to add that carrot cake flavor we all know and love.
- Eggs: help these muffins retain their structure as well as add moisture.
- Pure Maple Syrup: instead of refined sugar, these healthier muffins are naturally sweetened with pure maple syrup.
- Plain yogurt: Use a plain yogurt for these muffins – full-fat or low-fat both work. You can also use Greek yogurt if you prefer. Yogurt helps make these healthier muffins runny.
- Avocado oil: we like to use avocado oil, olive oil or coconut oil in our baked goods.
- Carrot: you will need about 1-2 medium sized carrots for this recipe. I like to use the smallest size on my box grater because I like smaller pieces of carrot in muffins like this. Do not use pre-grated carrots.
- Raisins: use regular or golden raisins for this healthy muffin recipe. If you are not a fan of raisins – you can leave them out.
Variations
- Try different mixes: Feel free to add other toppings to these muffins instead of raisins. They are also great with walnuts, pumpkin seeds, pecans or shredded coconut.
- Use the applesauce: You can use applesauce instead of pure maple syrup to sweeten these muffins.
- Make Mini Muffins: Line a paper-lined mini muffin tin and fill with the batter. The recipe should make 24 mini muffins. Reduce the baking time to 10-12 minutes.
- Add the Frosting: for an extra special treat, you can add this healthy cream cheese frosting (made with Greek yogurt) to the top of these muffins once they’ve cooled to room temperature. Healthier cupcakes are made!
How to Make Healthy Carrot Muffins
These healthy carrot muffins are easy to assemble in just a few steps.

Preheat the oven: Preheat the oven to 350 degrees Fahrenheit. Add paper liners to each of the muffin cups in your muffin pan. (I highly recommend using the liners instead of just adding cooking spray to the muffin pan.)
Mix the dry ingredients: In a large bowl, add the oat flour, almond flour, baking powder, cinnamon, baking soda, salt, ginger and nutmeg. Stir with a whisk to combine.
Mix the wet ingredients: In a separate medium bowl, add the eggs, maple syrup, yogurt, oil and vanilla extract. Beat well to combine.
Combination: Add the egg mixture to the flour mixture and mix just until combined with a wooden spoon. Mix the grated carrot and raisins.
Fill the muffin pan and bake: Transfer the batter to the prepared muffin pan. Bake for 18-20 minutes or until center is set. (You can test with a toothpick – it’s done when it comes out clean except for a few crumbs.)
Storage
Refrigerator: store frozen muffins in an airtight container in the refrigerator for up to a week.
Freezer: Cooled muffins can be stored in a zip lock bag or freezer safe container for up to 6 months. Thaw in refrigerator overnight or heat in microwave for 30 seconds to 1 minute.

More healthy muffin recipes for you to enjoy
Try my other healthy muffin recipes:
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Preheat the oven to 350 degrees Fahrenheit. Line a muffin tray with paper.
In a large bowl, add the oat flour, almond flour, baking powder, cinnamon, baking soda, salt, ginger and nutmeg. Stir with a whisk to combine.
In a separate small bowl, add the large eggs, maple syrup, yogurt, oil and vanilla extract. Beat well to combine.
Add the egg mixture to the flour mixture and mix just until combined with a wooden spoon. Mix the grated carrot and raisins.
Transfer the batter to the prepared muffin pan. Bake for 18-20 minutes or until center is set. (You can test with a toothpick.) Let cool for at least 10 minutes in the pan before transferring to a wire rack to cool the rest of the way.
Serving: 1pancake | Calories: 200kcal | Carbohydrates: 25G | Protein: 5G | Fat: 10G | Fiber: 2G | Sugar: 9G